Molecular dynamics graphs

Quantities, which are selected from the Averages Only column and added to the Avg. graph column, will be written out and averaged, as described above, but will also be plotted on the molecular dynamics graph. To inspect the computed average value, select the quantity so that the outline appears around it and the average is displayed beside Value. 

Schlitter et al. 1994] Schlitter, J., Engels, M., Kruger, P. Targeted molecular dynamics A new approach for searching pathways of conformational transitions. J. Mol. Graph. 12 (1994) 84-89... 

Averages or plotted values at regular time intervals. You specify an Average/Graph period in the Molecular Dynamics Averages dialog box. 

Molecular dynamics is essentially a study of the evolution in time of energetic and structural molecular data. The data is often best represented as a graph of a molecular quantity as a function of time. The values to be plotted can be any quantity x that is being averaged over the trajectory, or the standard deviation, Dx. You can create as many as four simultaneous graphs at once. 

To overcome the limitations of the database search methods, conformational search methods were developed [95,96,109]. There are many such methods, exploiting different protein representations, objective function tenns, and optimization or enumeration algorithms. The search algorithms include the minimum perturbation method [97], molecular dynamics simulations [92,110,111], genetic algorithms [112], Monte Carlo and simulated annealing [113,114], multiple copy simultaneous search [115-117], self-consistent field optimization [118], and an enumeration based on the graph theory [119]. 

Figure 1 (Plate 1). A molecular view of a small section of a flat lipid bilayer generated by molecular dynamics simulations. The bilayers are composed of l-stearoyl-2-docosa-hexaenoyl-5M-g]ycero-3-phosphatidylcholine lipids, i.e. the sn 1 chain is 18 C atoms long and the sn2 chain has 22 carbons, including six cis double bonds. The hydrophobic core is in the centre of the picture, and the hydrated head-group regions are both on top and bottom of the view graph. The head group is zwitterionic and no salt has been added. From [102], Reproduced by permission of the American Physical Society. Copyright (2003)...

Figure 3.43. The time dependent electronic temperature Te, lattice temperature Tq. and adsorbate temperature defined as Tads = [EH /2kB following a 130 fs laser pulse with absorbed laser fluence of 120 J/m2 centered at time t = 0. The bar graph is the rate of associative desorption dY/dt as a function of t. Te and T are from the conventional two temperature model and 7 ads and dY/dl are from 3D first principles molecular dynamics with electronic frictions. From Ref. [101].

Marelius J, Kolmodin K, Feierberg I, Aqvist J (1998) Q a molecular dynamics program for free energy calculations and empirical valence bond simulations in biomolecular systems. J Mol Graph Model 16(4-6) 213-225, 261... 

Lu SY, Jiang YJ, Zou JW, Wu TX (2011) Molecular modeling and molecular dynamics simulation studies on pyrrolopyrimidine-based alpha-helix mimetic as dual inhibitors of MDM2 and MDMX. J Mol Graph Model 30467-178... 

Wen EZ, Hsieh MJ, Kollman PA, Luo R (2004) Enhanced ab initio protein folding simulations in Poisson-Boltzmann molecular dynamics with self guiding forces, J Mol Graph Model, 22 415—424... 

Tel. 617-495-4018, fax 617-495-1792, e-mail karplus huchel.bitnet Molecular dynamics package using Chemistry at Harvard Macromolecular Mechanics force field. Extensive scripting language for molecular mechanics, simulations, solvation, electrostatics, crystal packing, vibrational analysis, free energy perturbation (FEP) calculations, quantum mechanics/molecular mechanics calculations, stochastic dynamics, and graphing data. 

Okamoto, Y. Generalized-ensemble algorithms Enhanced sampling techniques for Monte Carlo and molecular dynamics simulations. J. Mol. Graph. Model. 2004, 22, 425-39. 

Perez-Montoto, L.G., Santana, L., Gonzalez-Diaz, H. Scoring function for DNA-drug docking of anticancer and antiparasitic compounds based on spectral moments of 2d lattice graphs for molecular dynamics trajectories. Eur. J. Med. Chem. 2009, 44(11), 4461. 

Figure 15.7 Longitudinal SWNT deformations at 77, 300, and 600 K as indicated by the distribution of C-C-C angles for the highlighted carbon atoms illustrated on a section of the SWNT wall. Each graph represents a distribution of C-C-C angle populations over 5000 steps of the 5.0 ps molecular dynamics (MD) simulation. The longitudinal C-C-C angle of a perfectly circular and straight armchair SWNT is 180°. (Reprinted with permission from Ref. [72] Copyr t 2001 by the American Chemical Society.)...

El-Bastawissy E, Knaggs MH, Gilbert IH (2001) Molecular dynamics simulations of wild-type and point mutation human prion protein at normal and elevated temperature. J Mol Graph Model 20 145... 

Gsponer J, Ferrara P, Caflisch A (2001) Flexibility of the murine prion protein and its Asp 178 Asn mutant investigated by molecular dynamics simulations. J Mol Graph Model 20 169... 

We first discuss the overall chemical process predicted, followed by a discussion of reaction mechanisms. Under the simulation conditions, the HMX was in a highly reactive dense fluid phase. There are important differences between the dense fluid (supercritical) phase and the solid phase, which is stable at standard conditions. Namely, the dense fluid phase cannot accommodate long-lived voids, bubbles, or other static defects, since it has no surface tension. Instead numerous fluctuations in the local environment occur within a timescale of 10s of femtoseconds. The fast reactivity of the dense fluid phase and the short spatial coherence length make it well suited for molecular dynamics study with a finite system for a limited period of time. Under the simulation conditions chemical reactions occurred within 50 fs. Stable molecular species were formed in less than a picosecond. We report the results of the simulation for up to 55 picoseconds. Figs. 11 (a-d) display the product formation of H2O, N2, CO2 and CO, respectively. The concentration, C(t), is represented by the actual number of product molecules formed at the corresponding time (. Each point on the graphs (open circles) represents a 250 fs averaged interval. The number of the molecules in the simulation was sufficient to capture clear trends in the chemical composition of the species studied. These concentrations were in turn fit to an expression of the form C(/) = C(l- e ), where C is the equilibrium concentration and b is the effective rate constant. From this fit to the data, we estimate effective reaction rates for the formation of H2O, N2, CO2, and CO to be 0.48, 0.08,0.05, and 0.11 ps, respectively. 

Isralewitz B, Baudry J, Gullingsrud J, Kosztin D, Schulten K (2001) Steered molecular dynamics investigations of protein function. J Mol Graph Model 19 13-25... 

Theory, which explicitly includes chromophore-chromophore electrostatic interactions, certainly makes a number of predictions that can be readily verified. The predicted maxima in graphs of the electro-optic coefficient versus number density indicate that there is an ideal size for spherically shaped chromophores characterized by specific dipole moments, polarizabilities, and ionization potentials. More advanced calculations suggest that prolate ellipsoidal shapes are the least favorable for optimizing optical nonlinearily. Both spherical and oblate ellipsoidal shapes offer advantages. Finally, calculations suggest that to understand fully the observed poling behavior, including temporal behavior, molecular dynamics must be taken into account. 

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